The official Sucuri WordPress plugin comes with a tools that checks the integrity of the core WordPress files which are the PHP, JavaScript, CSS, and other files that comes originally in the official releases. The core integrity checks are powered by two main parts, a HTTP request that communicates with an official WordPress API service and an implementation of a checksum reader.

A checksum or hash sum is a small-size datum from a block of digital data for the purpose of detecting errors which may have been introduced during its transmission or storage. It is usually applied to an installation file after it is received from the download server - Definition from WikiPedia.

The plugin uses this checksum to detect if a file has been added, modified, or deleted. You must know that the plugin only checks check content of the PHP files under the document root directory, the inclusion and admin folders, so files under the content directory or others are not being checked because they are obviously not part of the official WordPress archives.

Explanation of the Warning

Consider the scenario where you have two files named abc.txt and xyz.txt with the content "Lorem ipsum dolor" and "Hello world" respectively, bellow you will see the execution of the command md5sum which provides a (virtually) unique identifier for the data inside each file. This example is very simple but in other scenario you would not have the time and patience to check the content of each file by hand so you would just scan the directory and retrieve the checksum of all the files inside it, then compare them with the checksum of the original file, this is very common when you are downloading data from the Internet.

Every time you create a file with the same data it will have the same unique identifier, the name of the files is not relevant for the evaluation so you could have twenty files with the text "Hello world" all with different names and all of them will result with the same checksum.

Comparing the checksum of a file you can learn if someone have modified its content, which is pretty common when a malicious person attacks your website and gets access to an administrative resource like the credentials of a user, he/she will try to keep the access even if these credentials are changed so he/she hides a malicious code generally known as a "backdoor" inside a core file.

What to do with Added Files

When a file is marked as added it means that it was not found in the official WordPress archives, at least not for the version number detected in your current website. For example, if your site has a file named wp-protect.php in the document root and the official WordPress archives do not come with this file it means that someone may have added that as a malicious thing.

However, some people like to upload a number of files in his website to facilitate its download, or for whatever reason you can think. In this case the file may not be malicious but the plugin does not knows that, it only cares about the integrity of the project not the content of the files.

At the bottom of the "Core Integrity" panel you will find a dropdown with a button that you can use to execute an action over the selected files from the table. For files that were added as added you can choose to delete them or mark them as fixed. If you do not trust the file(s) then a deletion is safe considering that they do not belong in the project and you do not know about them so there is no point to keep them. If you trust the file(s) then you can force the plugin to ignore them in future scans mark them as fixed.

What to do with Deleted Files

When a file is marked as deleted it means that it was found in the official WordPress archives, but not in the website. You will not see this mark frequently because when a file is deleted from the core directories the site generally goes down, but there may be some exceptions like the xmlrpc.php file which is used by WordPress to allow users and services to interact with the site through RPC.

In this case there is only one solution which is to restore the files fetching its original content from the official WordPress repositories. The plugin provides an option to do this automatically so you do not have to go through all the process to find the correct code for the version that your site is running.

What to do with Modified Files

When a file is marked as modified it means that it was found in the official WordPress archives and the website, but its content is different which is detected comparing their checksums. You should never modify core files of any project because this difficults the upgrades and maintainability of the code. If you find modified files you must select them all without hesitation and choose the option to restore their original content.